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made conversion functions to shorten code
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@eadlg2
eadlg2 committed Mar 4, 2024
1 parent 3adbc51 commit ecbe62a
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Showing 2 changed files with 113 additions and 67 deletions.
77 changes: 10 additions & 67 deletions src/box_model.py
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Original file line number Diff line number Diff line change
Expand Up @@ -11,6 +11,7 @@
from music_box_conditions import Conditions
from music_box_species_concentration import SpeciesConcentration
from music_box_reaction_rate import ReactionRate
import utils

class BoxModel:
"""
Expand Down Expand Up @@ -257,38 +258,9 @@ def readFromJson(self, path_to_json):
data = json.load(json_file)

# Set box model options
# make sure to convert the time units to minutes
chem_step_time = None
if 'chemistry time step [sec]' in data['conditions']['box model options']:
chem_step_time = float(data['conditions']['box model options']['chemistry time step [sec]']) / 60
elif 'chemistry time step [min]' in data['conditions']['box model options']:
chem_step_time = float(data['conditions']['box model options']['chemistry time step [min]'])
elif 'chemistry time step [hour]' in data['conditions']['box model options']:
chem_step_time = float(data['conditions']['box model options']['chemistry time step [hour]']) * 60
elif 'chemistry time step [day]' in data['conditions']['box model options']:
chem_step_time = float(data['conditions']['box model options']['chemistry time step [day]']) * 60 * 24

# make sure to convert the time units to hours
output_step_time = None
if 'output time step [sec]' in data['conditions']['box model options']:
output_step_time = float(data['conditions']['box model options']['output time step [sec]']) / 3600
elif 'output time step [min]' in data['conditions']['box model options']:
output_step_time = float(data['conditions']['box model options']['output time step [min]']) / 60
elif 'output time step [hour]' in data['conditions']['box model options']:
output_step_time = float(data['conditions']['box model options']['output time step [hour]'])
elif 'output time step [day]' in data['conditions']['box model options']:
output_step_time = float(data['conditions']['box model options']['output time step [day]']) * 24

# make sure to convert the time units to hours
simulation_length = None
if 'simulation length [sec]' in data['conditions']['box model options']:
simulation_length = float(data['conditions']['box model options']['simulation length [sec]']) / 3600
elif 'simulation length [min]' in data['conditions']['box model options']:
simulation_length = float(data['conditions']['box model options']['simulation length [min]']) / 60
elif 'simulation length [hour]' in data['conditions']['box model options']:
simulation_length = float(data['conditions']['box model options']['simulation length [hour]'])
elif 'simulation length [day]' in data['conditions']['box model options']:
simulation_length = float(data['conditions']['box model options']['simulation length [day]']) * 24
chem_step_time = utils.convert_time(data['conditions']['box model options'], 'chemistry time step') * 60
output_step_time = utils.convert_time(data['conditions']['box model options'], 'output time step')
simulation_length = utils.convert_time(data['conditions']['box model options'], 'simulation length')

grid = data['conditions']['box model options']['grid']

Expand Down Expand Up @@ -341,52 +313,23 @@ def readFromJson(self, path_to_json):
reactions.append(Reaction(name, reaction_type, reactants, products, A, B, D, E, Ea))

# Set initial conditions
# make sure to convert the pressure units to atm
pressure = 0
if 'initial value [Pa]' in data['conditions']['environmental conditions']['pressure']:
pressure = float(data['conditions']['environmental conditions']['pressure']['initial value [Pa]']) / 101325
elif 'initial value [atm]' in data['conditions']['environmental conditions']['pressure']:
pressure = float(data['conditions']['environmental conditions']['pressure']['initial value [atm]'])
elif 'initial value [bar]' in data['conditions']['environmental conditions']['pressure']:
pressure = float(data['conditions']['environmental conditions']['pressure']['initial value [bar]']) * 0.986923
elif 'initial value [kPa]' in data['conditions']['environmental conditions']['pressure']:
pressure = float(data['conditions']['environmental conditions']['pressure']['initial value [kPa]']) / 101.325
elif 'initial value [hPa]' in data['conditions']['environmental conditions']['pressure']:
pressure = float(data['conditions']['environmental conditions']['pressure']['initial value [hPa]']) / 1013.25
elif 'initial value [mbar]' in data['conditions']['environmental conditions']['pressure']:
pressure = float(data['conditions']['environmental conditions']['pressure']['initial value [mbar]']) / 1013.25

# make sure to convert the temperature units to K
temperature = 0
if 'initial value [K]' in data['conditions']['environmental conditions']['temperature']:
temperature = float(data['conditions']['environmental conditions']['temperature']['initial value [K]'])
elif 'initial value [C]' in data['conditions']['environmental conditions']['temperature']:
temperature = float(data['conditions']['environmental conditions']['temperature']['initial value [C]']) + 273.15
elif 'initial value [F]' in data['conditions']['environmental conditions']['temperature']:
temperature = (float(data['conditions']['environmental conditions']['temperature']['initial value [F]']) - 32) * 5/9 + 273.15
pressure = utils.convert_pressure(data['conditions']['environmental conditions']['pressure'], 'initial value')

temperature = utils.convert_temperature(data['conditions']['environmental conditions']['temperature'], 'initial value')

species_concentrations = []
for chem_spec, chem_spec_info in data['conditions']['chemical species'].items():
for chem_spec in data['conditions']['chemical species']:
match = filter(lambda x: x.name == chem_spec, species_from_json)
species = next(match, None)

# make sure to convert the concentration units to mol m-3
concentration = 0
if 'initial value [mol m-3]' in data['conditions']['chemical species'][chem_spec]:
concentration = float(chem_spec_info['initial value [mol m-3]'])
elif 'initial value [mol cm-3]' in data['conditions']['chemical species'][chem_spec]:
concentration = float(chem_spec_info['initial value [mol cm-3]']) * 1e3
elif 'initial value [molec m-3]' in data['conditions']['chemical species'][chem_spec]:
concentration = float(chem_spec_info['initial value [molec m-3]']) / 6.02214076e23
elif 'initial value [molec cm-3]' in data['conditions']['chemical species'][chem_spec]:
concentration = float(chem_spec_info['initial value [molec cm-3]']) * 1e3 / 6.02214076e23
concentration = utils.convert_concentration(data['conditions']['chemical species'][chem_spec], 'initial value')

species_concentrations.append(SpeciesConcentration(species, concentration))

# TODO: verify reaction rates
reaction_rates = []

for reaction in data['initial conditions']:
for reaction in data['conditions']['initial conditions']:
match = filter(lambda x: x.name == reaction.split('.')[1], reactions)
reaction = next(match, None)

Expand Down
103 changes: 103 additions & 0 deletions src/utils.py
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Original file line number Diff line number Diff line change
@@ -0,0 +1,103 @@
def convert_time(data, key):
"""
Convert the time from the input data to hours.
Args:
data (dict): The input data.
key (str): The key for the time in the input data.
Returns:
float: The time in hours.
"""
time = None
for unit in ['sec', 'min', 'hour', 'day']:
if f'{key} [{unit}]' in data:
time_value = float(data[f'{key} [{unit}]'])
if unit == 'sec':
time = time_value / 3600
elif unit == 'min':
time = time_value / 60
elif unit == 'hour':
time = time_value
elif unit == 'day':
time = time_value * 24
break
return time

def convert_pressure(data, key):
"""
Convert the pressure from the input data to atmospheres.
Args:
data (dict): The input data.
key (str): The key for the pressure in the input data.
Returns:
float: The pressure in atmospheres.
"""
pressure = None
for unit in ['Pa', 'atm', 'bar', 'kPa', 'hPa', 'mbar']:
if f'{key} [{unit}]' in data:
pressure_value = float(data[f'{key} [{unit}]'])
if unit == 'Pa':
pressure = pressure_value / 101325
elif unit == 'atm':
pressure = pressure_value
elif unit == 'bar':
pressure = pressure_value * 0.986923
elif unit == 'kPa':
pressure = pressure_value / 101.325
elif unit == 'hPa' or unit == 'mbar':
pressure = pressure_value / 1013.25
break
return pressure

def convert_temperature(data, key):
"""
Convert the temperature from the input data to Kelvin.
Args:
data (dict): The input data.
key (str): The key for the temperature in the input data.
Returns:
float: The temperature in Kelvin.
"""
temperature = None
for unit in ['K', 'C', 'F']:
if f'{key} [{unit}]' in data:
temperature_value = float(data[f'{key} [{unit}]'])
if unit == 'K':
temperature = temperature_value
elif unit == 'C':
temperature = temperature_value + 273.15
elif unit == 'F':
temperature = (temperature_value - 32) * 5/9 + 273.15
break
return temperature

def convert_concentration(data, key):
"""
Convert the concentration from the input data to molecules per cubic centimeter.
Args:
data (dict): The input data.
key (str): The key for the concentration in the input data.
Returns:
float: The concentration in molecules per cubic centimeter.
"""
concentration = None
for unit in ['mol m-3', 'mol cm-3', 'molec m-3', 'molec cm-3']:
if f'{key} [{unit}]' in data:
concentration_value = float(data[f'{key} [{unit}]'])
if unit == 'mol m-3':
concentration = concentration_value
elif unit == 'mol cm-3':
concentration = concentration_value * 1e3
elif unit == 'molec m-3':
concentration = concentration_value / 6.02214076e23
elif unit == 'molec cm-3':
concentration = concentration_value * 1e3 / 6.02214076e23
break
return concentration

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